SerialEM HowTo: Off-line Target Picking

Chen Xu

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In this document, I try to show you how to setup a dummy instance of SerialEM for picking more target points while main instance of SerialEM is busy collecting data for the points previously defined. With the latest beta version of SerialEM, one can easily add more target points off-line: either from the same computer or from a local computer at user site.

You can also get pdf version of this document here.


Table of Contents
1 The Background
2 The Setup
3 How to use it

1 The Background

One of the ways to define target for data collection is to manually pick good points in a medium mag montage map. Later, SerialEM drives stage to these positions using Realign routine which is very robust and reliable. It might take some time to pick all the interested point, but it is perhaps the only way to make sure you will be on the target precisely. For filament object, this way is also preferred.

It would be ideal to be able to pick good target positions while SerialEM is collecting data. And, for SerialEM running on a stable microscope like Titan Krios, data collection can be fully automatic, user is no longer required to babysit the data collection session on site. It could be very attractive to let user pick their preferred positions remotely without too much trouble of delay and lagging. Therefore, a setup which allows off-line picking becomes reasonably needed.

However, one could not do this with previous version of SerialEM. While SerialEM is busy collecting data, the navigator dialog window is gray out unless the action is stopped or pulsed. Fortunately, this is available with the latest beta version of SerialEM which allows more than one instance for this particular purpose.